Prions are a novel class of "infectious" pathogens distinct from viroids and viruses with respect to both their structure and the neurodegenerative diseases that they cause. Prion diseases are manifest as sporadic, inherited, and infectious disorders including scrapie, mink encephalopathy, chronic wasting disease, bovine spongiform encephalopathy, feline spongiform encephalopathy, and exotic ungulate encephalopathy of animals as well as kuru, Creutzfeldt-Jakob Disease (CJD), Gerstmann-Straussler-Scheinker syndrome, and fatal familial insomnia of humans. The prion protein (PrP) is the major, if not the only, component of prions. PrP exists in two isoforms: the normal cellular form (PrPC) and the abnormal disease (scrapie)-related form (PrPSc). Stan Prusiner and I began a collaboration to study the sequences of the prion proteins from various animals. This led to a study of the biophysical properties of the protein isoforms and peptides derived from the prion protein sequence. Analysis of these sequences by a variety of secondary structure prediction algorithms developed in our group and elsewhere offered an unusual result. While all of the algorithms agreed upon the location of the secondary structure elements, they disagreed as to whether a region would form an alpha-helix or a beta-structure. This suggested that the normal form, PrPC, and the disease causing form, PrPSc, might differ only in their structural conformation. Extensive experiments to detect distinctions in the covalent structure continue to be unrevealing. We knew that PrP 27-30, a proteolytically processed version of PrPSc that retained infectivity was rich in beta-structure and therefore hypothesized that the molecular etiology of disease could be a consequence of an alpha-helix to b-sheet structural transition. Peptides derived from the putative alpha-helical structural regions were synthesized and shown to form beta-sheets and amyloid reminiscent of PrP27-30. Spectroscopic studies of purified PrPC demonstrated that the normal cellular form was rich in alpha-helical structure and devoid of beta-sheets while PrPSc, the disease causing form, was enriched in beta-structure. These results lent credence to the notion that a conformational change was at the heart of Prion diseases. In an effort to understand these conformational changes in more detail and guided by a variety of spectroscopic and genetic data, we have used de novo modeling techniques developed by our group to produce a plausible model of the three-dimensional structure of PrPC. A heuristic approach consisting of the prediction of secondary structures and of an evaluation of the packing of secondary elements was used to search for plausible tertiary structures. After a series of experimental and theoretical constraints were applied, four structural models of four-helix bundles emerged. A group of amino acids within the four predicted helices were identified as important for tertiary interactions between helices. Among four plausible structural models for PrPC, the X-bundle model seemed to correlate best with the known point mutations that occur in the putative helical regions, and segregate with the inherited prion diseases. These 5 (of 11) mutations cluster around a central hydrophobic core in the X-bundle structure. The three-dimensional structure of PrPC that we proposed now provides a basis for rationalizing mutations of the PrP gene in the inherited prion diseases and a guide for the design of genetically engineered PrP molecules for further experimental studies. Interactive molecular graphics have played a crucial role in our modeling experiements and the visualization of our proposed three-dimensional structure of PrPC.